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Simon Pearce 78e2e76b24
New module: ichorCNA (#1182) 
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/hmmcopy/mapcounter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/hmmcopy/mapcounter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* ichorCNA run

* Add panel of normals code

* Try and fix tests

* Edit string detection in tests

* Fix linting issues

* Just failing END_VERSIONS

* Fixed versions.yml

* Added DOI

* Optional name for file

* Add when command

* Updated when

* Update modules/ichorcna/createpon/main.nf

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-02-11 16:56:13 +01:00
..
abacas Add when: block (#1261) 2022-02-04 09:53:32 +01:00
adapterremoval Add when: block (#1261) 2022-02-04 09:53:32 +01:00
agrvate Add when: block (#1261) 2022-02-04 09:53:32 +01:00
allelecounter Add when: block (#1261) 2022-02-04 09:53:32 +01:00
amps Add when: block (#1261) 2022-02-04 09:53:32 +01:00
arriba Add when: block (#1261) 2022-02-04 09:53:32 +01:00
artic Add when: block (#1261) 2022-02-04 09:53:32 +01:00
assemblyscan Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ataqv/ataqv Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bakta Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bamaligncleaner Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bamcmp Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bamtools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bamutil/trimbam Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bandage/image Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bbmap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bcftools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bedtools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bismark Add when: block (#1261) 2022-02-04 09:53:32 +01:00
blast Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bowtie Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bowtie2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bwa Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bwamem2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
bwameth Add when: block (#1261) 2022-02-04 09:53:32 +01:00
cat Add when: block (#1261) 2022-02-04 09:53:32 +01:00
cellranger Add when: block (#1261) 2022-02-04 09:53:32 +01:00
checkm/lineagewf Add when: block (#1261) 2022-02-04 09:53:32 +01:00
chromap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
clonalframeml Add when: block (#1261) 2022-02-04 09:53:32 +01:00
cmseq/polymut Add when: block (#1261) 2022-02-04 09:53:32 +01:00
cnvkit/batch Add when: block (#1261) 2022-02-04 09:53:32 +01:00
cooler Add when: block (#1261) 2022-02-04 09:53:32 +01:00
csvtk Add when: block (#1261) 2022-02-04 09:53:32 +01:00
custom Add when: block (#1261) 2022-02-04 09:53:32 +01:00
cutadapt Add when: block (#1261) 2022-02-04 09:53:32 +01:00
damageprofiler Add when: block (#1261) 2022-02-04 09:53:32 +01:00
dastool Add when: block (#1261) 2022-02-04 09:53:32 +01:00
dedup Add when: block (#1261) 2022-02-04 09:53:32 +01:00
deeparg Add when: block (#1261) 2022-02-04 09:53:32 +01:00
deeptools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
deepvariant Add when: block (#1261) 2022-02-04 09:53:32 +01:00
delly/call Add when: block (#1261) 2022-02-04 09:53:32 +01:00
diamond Add when: block (#1261) 2022-02-04 09:53:32 +01:00
dragmap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
dragonflye Add when: block (#1261) 2022-02-04 09:53:32 +01:00
dshbio Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ectyper Add when: block (#1261) 2022-02-04 09:53:32 +01:00
emmtyper Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ensemblvep Add when: block (#1261) 2022-02-04 09:53:32 +01:00
expansionhunter Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fargene Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fastani Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fastp Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fastqc Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fastqscan Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fasttree Add when: block (#1261) 2022-02-04 09:53:32 +01:00
fgbio Add when: block (#1261) 2022-02-04 09:53:32 +01:00
filtlong Add when: block (#1261) 2022-02-04 09:53:32 +01:00
flash Add when: block (#1261) 2022-02-04 09:53:32 +01:00
freebayes Update intervals (#1278) 2022-02-10 10:34:22 +01:00
gatk4 Update intervals (#1278) 2022-02-10 10:34:22 +01:00
genmap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
genrich Add when: block (#1261) 2022-02-04 09:53:32 +01:00
gffread Add when: block (#1261) 2022-02-04 09:53:32 +01:00
glnexus Add when: block (#1261) 2022-02-04 09:53:32 +01:00
graphmap2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
gstama Add when: block (#1261) 2022-02-04 09:53:32 +01:00
gtdbtk/classifywf Add when: block (#1261) 2022-02-04 09:53:32 +01:00
gubbins Add when: block (#1261) 2022-02-04 09:53:32 +01:00
gunc Add when: block (#1261) 2022-02-04 09:53:32 +01:00
gunzip Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hicap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hifiasm Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hisat2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hmmcopy Add when: block (#1261) 2022-02-04 09:53:32 +01:00
hmmer/hmmalign Add when: block (#1261) 2022-02-04 09:53:32 +01:00
homer Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ichorcna New module: ichorCNA (#1182) 2022-02-11 16:56:13 +01:00
idr Add when: block (#1261) 2022-02-04 09:53:32 +01:00
imputeme/vcftoprs Add when: block (#1261) 2022-02-04 09:53:32 +01:00
iqtree Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ismapper Add when: block (#1261) 2022-02-04 09:53:32 +01:00
isoseq3 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ivar Add when: block (#1261) 2022-02-04 09:53:32 +01:00
jupyternotebook Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kallisto/index Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kallistobustools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
khmer/normalizebymedian Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kleborate Add when: block (#1261) 2022-02-04 09:53:32 +01:00
kraken2/kraken2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
krona Add when: block (#1261) 2022-02-04 09:53:32 +01:00
last Add when: block (#1261) 2022-02-04 09:53:32 +01:00
leehom Add when: block (#1261) 2022-02-04 09:53:32 +01:00
lima Add when: block (#1261) 2022-02-04 09:53:32 +01:00
lissero Add when: block (#1261) 2022-02-04 09:53:32 +01:00
lofreq Add when: block (#1261) 2022-02-04 09:53:32 +01:00
macrel/contigs Add when: block (#1261) 2022-02-04 09:53:32 +01:00
macs2/callpeak Add when: block (#1261) 2022-02-04 09:53:32 +01:00
malt Add when: block (#1261) 2022-02-04 09:53:32 +01:00
maltextract Add when: block (#1261) 2022-02-04 09:53:32 +01:00
manta feat: nicer syntax (#1286) 2022-02-11 16:07:52 +01:00
mapdamage2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
mash Add when: block (#1261) 2022-02-04 09:53:32 +01:00
mashtree Add when: block (#1261) 2022-02-04 09:53:32 +01:00
maxbin2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
medaka Add when: block (#1261) 2022-02-04 09:53:32 +01:00
megahit Add when: block (#1261) 2022-02-04 09:53:32 +01:00
meningotype Add when: block (#1261) 2022-02-04 09:53:32 +01:00
metabat2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
metaphlan3 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
methyldackel Add when: block (#1261) 2022-02-04 09:53:32 +01:00
minia Add when: block (#1261) 2022-02-04 09:53:32 +01:00
miniasm Add when: block (#1261) 2022-02-04 09:53:32 +01:00
minimap2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
mlst Add when: block (#1261) 2022-02-04 09:53:32 +01:00
mosdepth Update mosdepth (#1256) 2022-02-09 12:45:55 +00:00
msisensor Add when: block (#1261) 2022-02-04 09:53:32 +01:00
msisensorpro Add msisensorpro (#1267) 2022-02-09 21:05:49 +01:00
mtnucratio Add when: block (#1261) 2022-02-04 09:53:32 +01:00
multiqc Bump multiqc version 1.12 (#1282) 2022-02-11 09:44:13 +01:00
mummer Add when: block (#1261) 2022-02-04 09:53:32 +01:00
muscle Add when: block (#1261) 2022-02-04 09:53:32 +01:00
nanolyse Add when: block (#1261) 2022-02-04 09:53:32 +01:00
nanoplot Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ncbigenomedownload Add when: block (#1261) 2022-02-04 09:53:32 +01:00
nextclade Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ngmaster Add when: block (#1261) 2022-02-04 09:53:32 +01:00
nucmer Add when: block (#1261) 2022-02-04 09:53:32 +01:00
optitype Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pairix Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pairtools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pangolin Add when: block (#1261) 2022-02-04 09:53:32 +01:00
paraclu Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pbbam/pbmerge Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pbccs Add when: block (#1261) 2022-02-04 09:53:32 +01:00
peddy Add when: block (#1261) 2022-02-04 09:53:32 +01:00
phantompeakqualtools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
phyloflash Add when: block (#1261) 2022-02-04 09:53:32 +01:00
picard Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pirate Add when: block (#1261) 2022-02-04 09:53:32 +01:00
plasmidid Add when: block (#1261) 2022-02-04 09:53:32 +01:00
plink Add when: block (#1261) 2022-02-04 09:53:32 +01:00
plink2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pmdtools/filter Add when: block (#1261) 2022-02-04 09:53:32 +01:00
porechop Add when: block (#1261) 2022-02-04 09:53:32 +01:00
preseq/lcextrap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
prodigal fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
prokka Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pycoqc Add when: block (#1261) 2022-02-04 09:53:32 +01:00
pydamage Add when: block (#1261) 2022-02-04 09:53:32 +01:00
qcat Add when: block (#1261) 2022-02-04 09:53:32 +01:00
qualimap Add when: block (#1261) 2022-02-04 09:53:32 +01:00
quast Add when: block (#1261) 2022-02-04 09:53:32 +01:00
racon Add when: block (#1261) 2022-02-04 09:53:32 +01:00
rapidnj Add when: block (#1261) 2022-02-04 09:53:32 +01:00
rasusa Add when: block (#1261) 2022-02-04 09:53:32 +01:00
raven Add when: block (#1261) 2022-02-04 09:53:32 +01:00
raxmlng Add when: block (#1261) 2022-02-04 09:53:32 +01:00
rmarkdownnotebook Add when: block (#1261) 2022-02-04 09:53:32 +01:00
roary Add when: block (#1261) 2022-02-04 09:53:32 +01:00
rsem Add when: block (#1261) 2022-02-04 09:53:32 +01:00
rseqc Add when: block (#1261) 2022-02-04 09:53:32 +01:00
salmon Add when: block (#1261) 2022-02-04 09:53:32 +01:00
samblaster Add when: block (#1261) 2022-02-04 09:53:32 +01:00
samtools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
scoary Add when: block (#1261) 2022-02-04 09:53:32 +01:00
seacr/callpeak Add when: block (#1261) 2022-02-04 09:53:32 +01:00
seqkit/split2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
seqsero2 Add when: block (#1261) 2022-02-04 09:53:32 +01:00
seqtk Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sequenzautils Add when: block (#1261) 2022-02-04 09:53:32 +01:00
seqwish/induce Add when: block (#1261) 2022-02-04 09:53:32 +01:00
shovill Add when: block (#1261) 2022-02-04 09:53:32 +01:00
snpdists Add when: block (#1261) 2022-02-04 09:53:32 +01:00
snpeff Add when: block (#1261) 2022-02-04 09:53:32 +01:00
snpsift/split Add when: block (#1261) 2022-02-04 09:53:32 +01:00
snpsites Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sortmerna Add when: block (#1261) 2022-02-04 09:53:32 +01:00
spades Add when: block (#1261) 2022-02-04 09:53:32 +01:00
spatyper Add when: block (#1261) 2022-02-04 09:53:32 +01:00
sratools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
staphopiasccmec Add when: block (#1261) 2022-02-04 09:53:32 +01:00
star Add when: block (#1261) 2022-02-04 09:53:32 +01:00
strelka Update intervals (#1278) 2022-02-10 10:34:22 +01:00
stringtie Add when: block (#1261) 2022-02-04 09:53:32 +01:00
subread/featurecounts Add when: block (#1261) 2022-02-04 09:53:32 +01:00
svdb Add svdb/merge (#1233) 2022-02-04 15:29:44 +01:00
tabix Update intervals (#1278) 2022-02-10 10:34:22 +01:00
tbprofiler/profile Add when: block (#1261) 2022-02-04 09:53:32 +01:00
tiddit Add when: block (#1261) 2022-02-04 09:53:32 +01:00
transdecoder Add when: block (#1261) 2022-02-04 09:53:32 +01:00
trimgalore Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ucsc Add when: block (#1261) 2022-02-04 09:53:32 +01:00
ultra/pipeline Add when: block (#1261) 2022-02-04 09:53:32 +01:00
umitools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
unicycler Add when: block (#1261) 2022-02-04 09:53:32 +01:00
untar Add when: block (#1261) 2022-02-04 09:53:32 +01:00
unzip Add when: block (#1261) 2022-02-04 09:53:32 +01:00
variantbam Add when: block (#1261) 2022-02-04 09:53:32 +01:00
vcfanno Add when: block (#1261) 2022-02-04 09:53:32 +01:00
vcflib/vcfuniq Add when: block (#1261) 2022-02-04 09:53:32 +01:00
vcftools Add when: block (#1261) 2022-02-04 09:53:32 +01:00
yara Add when: block (#1261) 2022-02-04 09:53:32 +01:00